Hidden By The Roots
by Calzohh
Summary: The World is different. In the midst of the ruins of their home the Konoha 11, led by Jiraiya of the Sannin move to secure a weapon to help repel their enemies. Deep in the roots of the hidden leaf a beast stirs, outside and within the walls enemies gather. This is the Fourth Shinobi War. Konoha Stands Alone. The Will of Fire continues to burn... But for how long?
1. Author Notes

Author Notes:

Disclaimer: I don't own Naruto. Obviously.

Notes/Warning: This is an AU. Characters will be OOC, Characters will die, History will be inaccurate. Certain characters will be way more powerful while others may be weaker. Characters that don't know one another or have brief talks may be friends or more.

I'll try not to get too bogged down in irrelevant history in the story, but I'm open to questions about my view of the world.

This fic will also mostly be written in Japnenglish which means Japanese jutsu names and titles but English dialogue and description. If there is a lapse in this and a title is written in English instead (i.e Lord fourth instead of Yondaime-Sama) I apologise.

Pairings will be… undecided for now but I do know that just because characters are together or get together doesn't mean they'll stay together. I'll list the notable differences below: Spoilers if you haven't finished the series obviously.

There is No Zetsu or Kaguya resurrection plot, they'll be mentioned as will the Sage of Six paths but not as major plot drivers, The Ōtsutsuki clan will be mentioned and may even show up but only if I decide later on.

Hashirama killed Madara at the Valley of the End. This means Obito died in that cave.

The Kyuubi will have escaped during Naruto's birth, the full details will be revealed.

The Fourth shinobi war is basically Suna, Kumo, Taki, Oto, Iwa and Kiri against Konoha. Which is why the fic will start.

The younger generation will not know about the Kyuubi or Naruto has he won't have grown up with them. In this fic there is no civilian council, just the Hokage – his three advisors (Danzo, Homura and Koharu) and the clan heads. (Hyuuga, Uchiha, Senju, Nara, Yamanaka, Akimichi, Sarutobi, Kurama Inzuka, Aburame. Though in the end of everything the Hokage has the final say. That being said sometimes a leader bending to the will of the people is necessary as you'll see in the fic.

Sasuke will be a good little leaf shinobi, Itachi will be dead as will some of his clan, not all. This means Sasuke will not be leaving the village in this fic, the reason being he is never pushed by Naruto and never grows jealous, in this fic he will be Kakashi's apprentice and a loyal ninja, which means Karin, Juugo and Suigetsu will remain with Orochimaru in Oto. He will have beaten Itachi in a mission and have taken his eyes after he was told the truth of the massacre, in this story, Sasuke will have the EMS from the start and will be Konoha's flagship for the next generation.

Other characters will be also be alive or have lived longer than Canon, Hizashi Hyuuga will have lived longer in this story for example.

Tsunade will be Hokage at the start of the fiction but there will be flashbacks. The leaders of each village will be:

Suna and Taki: Gaara

Kumo: Ay

Iwa: Onoki

Kiri: Yagura

There is no Evil Akatsuki. Characters in the group may show up but not to take all the Bjuu. Whether that means Pain exists I haven't decided yet.

Power Ratios for certain characters will be changed, Mainly the Bjuu. The biggest example being that the Kyuubi will by far be the most powerful. Granted it's like that in the anime given that Naruto laid the smackdown on Two to Seven tails with only half of the Kyuubi inside him. Keep in mind it doesn't mean Naruto will win every fight and it doesn't mean a C rank opponent cant take on an A rank, it depends on their fight style and for Jinchurki their control (Yugito could beat Fuu since she has mastery over her Bjuu Chakra). The Kage will be stronger too, as will Kakashi and the Jonin Sensei, because I've never really liked the development behind characters like Asuma and Kurenai. Same for back ground characters like Yugao, Hayate, Genma ect.

Naruto will not be friends with Kurama, they'll be partners and he'll be a powerful ninja without that chakra, Naruto isn't evil, but he certainly isn't good. He was raised as the perfect weapon. So obviously without his influence, characters will be different, Sasuke and Hinata being the most obvious examples though you will see early on that other characters have entirely different fates.

Naruto will have five chakra natures and full control over Kurama's chakra (Both Yin and Yang, this is my way of balancing out the lack of Kenkei Genkai like Son Goku or Saiken offers their Jinchuriki) , though his transformation will be more like Killer B's instead of the Chakra mode he has in the anime. He will still have the Kage Bunshin and Rasengan but he will use them in conjunction with multiple jutsu's and kenjutsu. His appearance will be more rugged and his personality a little hard and rougher.


	2. Chapter One

The sounds of muffled coughing and the tearing of skin filled the night air as Sasuke Uchiha, loyal Uchiha and Avenger of the fallen members of his clan, ended a Kumo-nins life. He waited a moment further to see if his kill drew any attention before he stood, the light of the battle field showing his full form. His red sharingan blazing in the darkness as he looked out across his home, Konohagakure no Sato, the village was a war ground, the sounds of battle raging around them, though it had quieted in this portion of the village, when the invaders took the city walls the ninja were forced to retreat activating small counter measures to slow the advance and give them more time. They couldn't abandon their home, of course that was an advantage. The village was their home and that meant that they knew it better than anyone else. The forests, the back alleys, the tunnels and the roof tops were theirs and they made damn well sure to use that to their advantage. His red eyes moved up the Hokage Monument, the leaders of the past and present vigilantly standing watch over the burning village. His eyes fell on the first face, memorising the destroyed face of Hashirama Senju, the first Hokage co-founder of the village along with his forefather Madara Uchiha. Together two warring clan members and rivals had come together to make this. Konoha. The village hidden in the leaves. The very formation of the village lead to the formation of the five hidden villages and subsequently the world as he knew it.

Despite best efforts in maintaining peace, the rivalry between Hashirama and Madara boiled over until it came to blows, the battle between the two gods amongst men left a scar in the very earth, the battle lasted three days as Madara fought with his Eternal Mangenkyou Sharingan against the Mokuton of the first Hokage, Madara had used a powerful genjutsu on the mightiest of the Tailed Beasts, the Kyuubi, a nine tailed fox whos very presence was enough to kill people, its chakra so volatile and acidic it could kill with contact, the battle was brought to a halt when Mito Uzumaki sealed the Kyuubi inside herself to save her husband and thus became the first recorded Jinchuriki, a human sacrifice, Madara was killed on the banks of the newly created river by his best friend. Hashirama was never the same after that, he governed with the help of his brother, Tobirama Senju. and wife. Of course with several groups of organized ninja leading what was essentially mercenary villages, disputes began, the first shinobi war began and with it came the death of the Shodai Hokage. His eyes fell on the wreckage of the second face. , Tobirama Senju, the end of the war came and for a while there was peace, under the Nidaime Hokage the village flourished, he put forth decree's that revolutionized the village and also created the Shinobi Academy, The ANBU and the council to give all the clans a voice, until during what was supposed to be a peace treaty between Konoha and Kumo turned out to be an ambush, he named his successor, his student Hiruzen Sarutobi, a man who would become known as the second Kami no Shinobi to become the Sandaime Hokage and with those final words of wisdom he left to face his death, the gold and silver brothers of Kumo, Kinkaku and Ginkaku. His face moved over to the man who had been Hokage for most of his life, a small ball of conflict arose in his chest. The same man most of the village saw as nothing more than a kind old man, was the same man who had ordered the deaths of his family. most of it anyway.

His reign began with a war, and it gave birth to many legendary shinobi such as the Dentetsu no Sannin and the White Fang and eventually another victory for Konoha. Years passed once more and Sandaime fought not only for peace and prosperity between nations, he was ultimately unsuccessful when after an unfortunate mission failure by the White Fang, the third great shinobi war began, this was to be the deadliest war yet, all five villages fought in brutal and vicious warfare spanning three decades, the battles giving birth to the legendary Ino-Shika-Cho, Sharingan no Kakashi, The Bloody Red Habanero and to the man who would eventually become the Yondaime Hokage Minato Namikaze, Konoha's yellow flash, slowly the fighting slowed and eventually one by one nations dropped out of the war too drained of both men and resources to continue fighting till only Konoha and Iwa remained, it was then Minato Namikaze would make his name known throughout the world as he gained the first ever SS ranking in the bingo book, using one jutsu, the yellow flash slaughtered over three thousand men in minutes with only minimal assistance, teleporting in flashes of bright yellow light and leaving blood and destruction in his wake, the war ended less than a week later, minor conflicts popped up after wars but nothing major. The Yondaime was crowned, the youngest Hokage ever and the strongest since Hashirama Senju himself, praised as the second coming of first Hokage with the potential to end the cycle hatred that plagued the shinobi world. The people celebrated the victory they gained... though his reign was to be the shortest, disaster struck the village when one night on October tenth, the Kyuubi no yoko appeared in the centre of the village without warning, civilian attempted to flee but many were killed anyway, crushed in the fierce battle between the shinobi of Konoha and the large tailed beast, despite the effort of both Konoha's forces and their legendary soldiers, thousands died from mere exposure to the poisoned chakra that the survivors remembered to this day, Sasuke had once asked Kakashi what it felt like and he likened it to the very literal definition of hatred, suffocating rage and malice. Sasuke never asked about it again.

The battle was hard fought and eventually won when the Yondaime Hokage used a forbidden jutsu to kill the Kyuubi. His eyes scanned over the face of the Yondaime Hokage and he frowned, when he was younger his mother used to tell him stories of the man, then he'd learned of the man in school. Perhaps if he was still alive this wouldn't have happened. Sasuke shook his head clear of the thoughts and quickly began to move through the city trying to reach the rendezvous point. He arrived in a courtyard behind a small market. Two shadows appeared beside him, one was Shikamaru Nara, genius in every sense of the word, a master at the manipulation of shadows unlike anything his clan had ever seen and his current squad leader, known in the Bingo book as Konoha's Shadow Blade with an S ranking, Shikamaru Nara was one of the deadliest ninja's his age, the other was his old genin teammate Sakura Haruno, apprentice of Tsunade Senju, one of the Dentetsu no Sannin and Gondaime Hokage, known as the Slug Princess like her master she was a master medic and the only person besides Tsunade herself who could use her super strength, perfect chakra control and her own unique summoning of the Slug and master of the Strength of one hundred seal. Sasuke offered the two of them nods of acknowledgement before he spoke "They have patrols everywhere, we have to hurry, where are the others?" Sasuke asked causing Shikamaru to sigh "Jiraiya-sama and the others will arrive soon" he promised as he looked around. Sasuke looked at Sakura for a moment and spoke "Are you ok?" he asked her and she looked up at him with her green emerald eyes '_No' _they screamed like so many of his fellow shinobi "I am fine Sasuke-kun" he accepted the answer despite knowing it wasn't true, he had no other choice.

Despite the destruction of their home Sasuke knew they would be ok, his heart he knew because deep inside him as long as he had air to give, the will of fire burned inside him and his comrades. When they landed they heard a noise and they were joined by nine more people. Sasuke nodded to Sakura and they dropped their guard as the faces of their friends greeted them. Sasuke's sharingan scanned the war-torn faces of his comrades, first he saw Kiba Inuzuka and his dog Akamaru, the dogs white fur was drenched in the blood of their vanquished foes Kiba himself was not much better picking the flesh and gore of his enemies out from underneath his clawed finger nails, the chuunin gave Sasuke a short nod as they made eye contact. Next was Neji Hyuuga, his personal rival and friend when they had met they hated one another the rivalry of their clans strong between them as they were both considered prodigies, when they fought to a draw in the finals of their first chuunin exams they became training partners and from there a friendship grew. Next to him was Hinata Hyuuga, Clan heiress and unrivalled user of the gentle fist, he remembered her when she was younger, a timid girl, whatever shyness had taken root in her was beaten out of her by her clan, despite that she was still a good person, albeit cold at times Their piercing white eyes scanning the area for enemies, the Byakugan, the all seeing eye… the Sharingan's rival… it made Sasuke scoff, the Uchiha arrogance in him momentarily taking over before he let it go and he moved on. Next was Ino Yamanaka and Choji Akamichi, the other halves of Shikamaru's team and the next generation of the Ino-Shika-Cho, the hefty boy was once upon a time called fat, now he was a young man made of muscle, the young woman next to him despite being covered in grime held a certain aura of both beauty and danger and one wrong comment could show you how deadly she really was, each of them surpassed their fathers and had become deadly shinobi. He looked to Shino Aburame, part of the legendary clan of bug users, living as one with their insects and using them as weapons, the young man never failed to go unnoticed even amongst friends. Next was Rock Lee, to describe the thick browed man as anything less than eccentric was an insult and to make fun of his skills was even worse, even now the young ninja would shout about Youth as he pummelled his way through enemy ninjas like a hot knife through butter, his skill in taijutsu matched only by his more eccentric sensei Might Gai, his teammate stood next to him, her hair tied in her usual buns, a coupled of the senbon missing, she looked haggard but very much active, yet another young ninja unmatched in their field, as a weapons mistress, Tenten held more skill with anything that was put into her hands than most. The last member of their group was older, a legendary warrior, their current leader and one of the strongest shinobi Konoha had ever produced, Jiraiya the toad sage, second member of the Dentetsu no Sannin.

He began to move, and the rest fell in line without a word. They passed through the shadows heading towards the Hokage monument, it didn't take ling for them to reach it, there was hole at the base that hadn't been there before, bodies of departed ninja littered around it, Sasuke noted there were more foes dead than Leaf Shinobi. He cast his gaze upwards at the ruined face of the Yondaime which had been specifically targeted by Jutsu after Jutsu by Iwa Shinobi. The young Konoha 11 wouldn't ever forget the look in the eyes of their sensei's as the Yondaime's face crumbled, nor the fire I their eyes during the next engagement as they made the enemy pay for desecrating the face of one of their hero's. Sasuke stepped over the wreckage looking at the bodies around him, he saw one of the bodies face up, the blank white mask that adorned his face he recognised, signalling the fallen ninja as one of Danzo Shimura's Foundation, the roots of Konoha. Sasuke turned to Jiraiya and spoke "What is our mission?" he asked and Jiraiya paused a moment "Search and Retrieve, follow me and keep to the shadows, the less we disturb the better, the force is only so large because this cannot afford to fail" then he stepped into the hole in the wall. One by one the younger generation followed him until they were inside a maze of tunnels and junctions all showing signs of heavy fighting between the enemy invaders and the fanatic ninjas of the foundation. As they moved deeper into the bowels of their village Jiraiya turned them and spoke "You stay close to me, do not attempt to help any of the ANBU, we have our mission" He ordered in a stern voice, quiet "Hai" filled the air multiple times.

The Toad Sage levelled them all with a stare before he led them into the fray. The inside of the Root Base was a maze, Jiraiya referred to a crudely drawn map occasionally, the young ninja taking formation around him constantly shifting, they came across a large room with a heavily sealed door, the toad sage grinned and spoke "This is the first door, defend me while I open it" he spoke and the young men and women fell into formation, suddenly three masked men dropped from the ceiling, their blank ANBU masks and black cloaks concealing their weapons until they were brandishes "Authentication" Spoke the leader, his voice sounded young, he held a blank scroll and a brush, pushing chakra into it ready to battle should he need to. Jiraiya spoke slowly after signalling for his team to stand down "Sannin Kage Futon Doton Shodai" He spoke with assertion and when he finished the men stood up putting their weapons away "Jiraiya-Sama we were instructed to guard the vault and the prisoner at all costs by Danzo-Sama, what are our new orders?" the young man asked. "Fucking robots" Kiba mumbled earning nods from some of the other ninja around him but no reaction from the ROOT Ninja, then a voice echoed down the halls "There are more down here" it shouted and Jiraiya cursed under his breath "Buy us time to secure the Yondaime's legacy" he ordered and the masked ninja nodded before he rushed off with his team, Jiraiya began working on the seal, Sakura stood behind him "Jiraiya-Sama what do you mean secure the Yondaime's legacy?" she asked as she watched the hall that filled with sounds of heavy battle, it sounded like the Root ANBU were giving them hell. A sigh escaped the Toad Sage as he worked "This is the most closely guarded secret in the village, listen well for ill only speak it once" The white haired man continued his work on the seal as he spoke "You were taught in the academy that the Yondaime killed the Kyuubi using a forbidden jutsu, while my student defeated the Kyuubi he was unable to kill it" He said shocking the younger generation, some were tempted to speak but they knew better than to interrupt "Doing the only thing he could he summoned the Shinigami and used its power to seal the beast into a baby at the cost of his own life" This caused some of them to gasp, they understood but the mere act, Kiba was angry though it was to be expected, his clan was for the pack first and a sacrifice like that was unacceptable, as was Lee and Ino. Shikamaru, Neji and Sasuke understood why the fourth did it, the Hokage must always put the village first, their faith didn't waver, the rest were undecided until he spoke again "He sealed the beast into his newborn son" Jiraiya said earning more reactions of shock and anger, the second he said that he wished he hadn't, some of the younger ones were radiating killer intent, the women were, imagining what it would've been like to have their child damned to such a fate. The seal on the stone slowly began to pulse blue before the door slowly opened just as one of the masked ninja's bounded back into the room, he discarded his scroll and brush brandishing his Chokuto and gutting a ninja who lunged after him "Everyone inside now!" Sasuke yelled to get the shocked shinobi moving, they moved inside and once he joined them he pulled at the door with the help of Choji, the last thing they saw was the Root Shinobi being surrounded but continuing to fight despite the odds. Jiraiya moved forward and placed his hand on the stone "Fuiin!" he growled pumping his chakra into the stone. The seal seemed to glow and the Sannin spoke again.

"Come we don't have much time, that lock won't hold forever" He began to walk down a set of steps and after a moment the young shinobi followed him. "I can't believe the fourth sealed the Kyuubi inside his own son" Ino said her eyes looking towards the steps, her brow creased in thought. "It is most unyouthful" a sombre Rock Lee agreed. The rest were silent for a while before Tenten spoke "If this is the fourth's son, why is he locked up?" The weapons mistress asked, the Sannin didn't turn around as he answered "The child was supposed to be viewed as a hero, the Sandaime was supposed to keep him safe till he could claim his father's legacy…" the Sannin's voice sounded almost sad now, of course they knew the man had trained the Yondaime "The council refused instead voting to have the child forged into a weapon or executed, having only two options, Sensei decided to have the child killed instead of having Minato's legacy corrupted" He said causing many of the Konoha ninja to question their faith in the old man, they remembered him as kind old man, the professor. Jiraiya knew different as did Sasuke, he knew that his sensei was a cunning and manipulative old bastard who could order your whole clan exterminated and play the part of grieving leader at the funeral the next day. The toad sage and self-proclaimed super pervert looked back at the children "Then we found out how powerful the Kyuubi really was" he said his eyes darkening as he spoke.

_The Village was barely kept in order, the smoke of fires lit in the battle still smoked as rescue teams combed the ruins for survivors. Among the dead was their honorable fourth hokage Minato Namikaze and his wife Kushina Uzumaki. Hiruzen's old heart ached at the mere mention of their loss, He'd also lost his wife and his eldest son had been injured, his career as a shinobi was over. He sighed and filled his pipe and was about to light it when a loud cry pierced the room. He stood up and walked over the crib and gazed down at the baby inside. He was small, too small Hiruzen thought but they knew he would be like this, he was already two months premature, normally they'd have him hooked up into half a dozen different machines, but this baby was special. He had something far more powerful to heal him. The seal that held the great Kyuubi no Yoko was burned angrily into the skin of the baby, keeping him alive. The doctors that had examined him said trace amounts of the kyuubi's chakra was circulating through him, the child apparently was in excruciating pain as it bore the brunt of the Kyyubi's killing intent and malice, a side effect of Minato's seal. Hiruzen slowly bent down and picked up the crying baby trying to soothe him "Hold on Naruto-kun, we'll get you fed soon" He promised the crying baby before he spoke again "Neko" He called and young woman in a cat mask appeared "See him changed and fed before bringing him to the council room unharmed" the old man stressed receiving a nod before the baby was taken from him, he turned and spoke again "Inu" he said as another masked shinobi dropped from the shadows "Call a council meeting" he watched the woman leave before he moved back to his desk lighting the pipe he'd left behind before leaving his office, one he'd hoped would never be his again._

_The room was quiet as Hiruzen Sarutobi slowly moved to the head of the council room table and took the seat of the Hokage, wearing his full red and white robes, his old eyes scanned across the room to take in the remaining clan heads. Shikaku Nara, Choza Akimichi and Inoichi Yamanaka were the first three he looked at, the three waiting for him to speak. He shifted his gaze and found Tsume Inzuka and Shibi Aburame, his gaze shifted to the empty Senju seat and sighed, he had thought the village being attacked would bring his errant student home, but it didn't. Across the table was the seat of the Uchiha clan head Fugaku Uchiha, next to him sat Hiashi Hyuuga. He looked to his sides and saw his old Genin teammates Homura and Koharu, his trusted advisors. The last person of note he saw was his old rival and shadow Hokage Danzo Shimura. "The council is in session, I have decided to retake the Hokage position until the village is recovered" He declared before he looked at his Jonin commander "Shikaku damage report" The elderly Hokage ordered earning a tired sigh from the Nara clan head though no audible complaint, it appeared even that was too much work "The village center was levelled, sections of the wall suffered damage as well as several other key buildings, rescue efforts for trapped civilians have been underway since after the attack but most of it is body recovery" He reported and the Hokage nodded. More status reports were issued and eventually the doors opened and the council members eyes dell on the ANBU holding a crying baby. The baby was placed on the table in front of Hiruzen "Last night when Minato defeated the Kyuubi he used the Shiki Fuuijin to summon the Shinigami, at the cost of his own life he sealed the beast inside this baby" The third began as the clan heads began to stand he spoke again "This is Naruto Namikaze-Uzumaki, son of Kushina and Minato Namikaze" The silence in the room was only equal to the tension that weighed thick in the air, none spoke as they weighed their need for revenge against the beast that had decimated their home. So many of the clan heads had lost that night. The room was silent but for the cries of the baby. "Neko why is he crying so much?" Came the gravelly and level voice of Danzo Shimura, Hiruzen frowned, it was unlike his old team mate to ask such questions. "The Kyuubi's chakra is yet to settle completely, we believe the child is currently being filled with its chakra and is directly receiving the beasts killing intent" Neko reported, this seemed to ignite uncertainty in the council, the child would grow under the killing intent of the beast. "The council calls for vote on the fate of Hokage-Sama's child and the Jinchuriki of the Kyuubi. Options will be weighed and discussed before a vote will be carried out" the Hokage declared, he looked at the premature child, who was breathing easily between each loud scream, at least his lungs were working. The council session stretched, some clan heads wanted the child killed, the idea of allowing the child a normal life seemed to be the most common idea until a gravelly voice broke the conversation "Hiruzen, the child should be allowed to join my foundation, the tree has been weakened, this last war and now this disaster have crippled us, if we do not do something to strengthen our forces the fourth shinobi war may begin already, a war the great tree cannot withstand" Danzo's ease at discussing the enslavement of a baby not even a day old worried the council, but not enough for them to say his point was nonsense. "Ayes" echoed throughout the chamber and Hiruzen closed his eyes gesturing for Neko to hand him the screaming baby Naruto. He took the baby in his old hands and cradled him carefully. "The we vote… the child dies, or he becomes the weapons sword and shield" Hiruzen closed his eyes and the votes were cast. twelve clan heads voted… Hiruzen squeezed his old eyes closed tight so he couldn't see who cast what side "The votes are even, six split" Spoke the voice of Inu "Since the Senju clan head isn't present the vote falls to Hokage-Sama" _

_His breath froze in his old throat "Sorry Minato… Kushina… we have failed you.. Naruto… forgive me" Hiruzen whispered before he looked up his eyes cold and harsh as they found Danzo's own remaining eye. The room was silent as Hiruzen rose from his feet and retrieved a kunai from the inside of his robe "The child dies". He raised his hand and drove the Kunai downwards towards the child, suddenly he was the room was pulsed with heavy chakra and everyone was knocked away from the centre table. When Hiruzen rose he saw red wisps of chakra angrily surrounding the baby as it cried, its once blue human shaped eyes now an angry red slit much like the beast that had rampaged across the village._

Jiraiya found another door at the bottom of the steps heavily sealed "Sandaime-Sama did that?" Sakura asked with a light frown, before the Toad Sage could reply the Hyuuga Heiress did "Sandaime-Sama did what he believed to be right, a foolish notion, the child should've been weaponized" Hinata spoke simply, the others didn't like her words, muttering to themselves. "When Sarutobi-Sensei attempted to kill the child the Kyuubi fought back, using its chakra to shield the child, the seal meant if the Yondaime's child died the it did too" Jiraiya said "In the end he was weaponized". The hall was silent except his working at the door, the Konoha 11 debated their own philosophies against what was best for the village. Sasuke understood, his own brother died for the village, he valued it above everything except him. Itachi Uchiha would've done what was best for the village... Sasuke would follow that path to the end as his beloved Ni-Chan did. Sakura didn't like it much but she understood, her Sensei always spoke of the loss she endured for the village, her brother Nawaki, her lover Dan. To be a ninja is to endure, to walk the hard path so others don't have to. Hinata and Neji accepted it, it was the childs fate to be born that day, to carry this burden. Rock Lee refused to accept it, to him it was unyouthful. Kiba found himself questioning his will of fire as did Tenten and Choji. Shikamaru, Ino and Shino believed the decision the correct one, it was logical, that didn't mean they liked it. "Orochimaru once told me that the village was a meat grinder, feeding the young and old into it until there was nothing left… I didn't believe it until I met Naruto, he is the perfect shinobi… but a lot of blood was spilt to make him this way" Jiraiya opened the door and entire hall was flooded with potent killing intent, it stalled the young Shinobi. It wasn't until their leader spoke did they finally move "Do not believe anything you see in this next room, it appears the seal on Naruto's cell has degraded with the damage to the village, walk in a line, do not wander into the shadow's and don't speak to the voices or watch any illusion's" His voice was stern and left no room for argument before he began to walk into the darkness.

One by one the Konoha 11 walked into the darkness. It was quiet first, nothing but the sounds of footsteps of their company, then it slowly began, fingers brushed them as they walked past attempting coax them into the darkness, whispers of loved one's lost. Ino heard her mother who died in the first salvo. As did Hinata though this voice was telling her how disappointed she was in her. Neji heard his father, Rock-lee the anger of his beloved sensei. Sakura heard nothing, she couldn't be affected by the genjutsu, Shino's bugs prevented his exposure as well. Kiba heard his sister who'd been captured and kept as entertainment for days before she was found dead along with her dogs. Though each member suffered the voices of their past pain none suffered more than Sasuke who heard his clan cry out for vengeance. The voices of his cousin's aunts and uncles echoed in his head until he heard a dismissing grunt. He hadn't heard it in years. Sasuke turned and saw his father turn his back on him, he saw the bleeding wound Itachi had inflicted on him. He heard another noise and he turned and saw his cousin Shisui smiling at him, his eyes missing from his head and blood running down his face "Foolish little brother" he heard another voice and turned to find Itachi, clad in Akatsuki garb reaching for him. "Nii-Chan?" he asked in a strained tone, he reached out to take his older brother's hand then another grasped his collar pulling him roughly into another room. He saw his brother disappear and he went to move before another hand roughly pushed him down and he saw the angry eyes of his team mate "Baka! What did Jiraiya-Sama say?" she scolded him, he would've blushed in embarrassment had it not been for the fact they were surrounded by the others. He stood up and looked back at the door longingly before he looked at Jiraiya who shook his head "Don't feel bad kid, I imagine he has fooled many shinobi smarter than you with that horrid genjutsu" The man attempted to make him feel better, but it did little to ease his own thoughts. He looked forward and there was a long hall with a cage at the end, the cage was so dark it was hard to see past the bar's even with his sharingan active. Jiraiya moved forward and the rest followed cautiously "is that a visitor?" a dark voice asked that sent shivers down their spine "We don't get many visitors down here… even the Root Ninja stopped coming down here" a pale white hand gripped the bars of the cell.

Its nails were more like clear claws. Suddenly a pair of red slitted eyes appeared to float in the darkness. The younger ninja all froze as the eyes washed over them before they heard someone speak "Y-Y-You… it's y-you" Hinata Hyuuga spoke causing the others to turn their gaze to heiress, they hadn't heard the girl stutter since her early academy days. "You're the one who saved me." this seemed to shock everyone except Jiraiya. "Is that you little Hyuuga… my you've certainly grown up haven't you" the voice spoke the red eyes taking her in "I didn't recognize your chakra… it was once so timid and weak now tis the same as the rest of the Hyuuga" the red eyes flitted to Neji before a stern voice interrupted "You've tortured us enough Naruto, your time has come, you're being recalled to service the village in its time of need" Jiraiya spoke the red eyes flashed with fury before locking onto the Toad Sage, killing intent washed over those in the room. "Why would I do that? After you betrayed my father's wishes? This village deserves it's punishment!" as he spoke Naruto leaned forward, the younger shinobi gasped at the young man before them.

His face was a spitting image of the Yondaime. or it would've been had it not been for the jagged harsh whisker marks across his cheeks and the furious red eyes. He bared his teeth revealing the sharp canines for them to see. "Namikaze-san I know the village has treated you unyouthfully but w-"Rock-Lee began only for they eyes to flick to him "Detecting you was a little trickier.. I see why now, your chakra is so weak it's like you have none..." The lips of the Jinchuriki curled into a snarl "And that horrid Green jumpsuit… you must be Might-Gai's student… do not speak to me of the twisted ideals that man spouts" Lee's feature's twisted for a moment before Tenten's hand found his shoulder stopping him from replying. Jiraiya took the opportunity to take Naruto's attention "The Hokage has agreed to offer you whatever you want in return for your service in this trying time" Jiraiya said and the red orbs went back to him before Naruto spoke "Anything I want?" his voice was calm but his red orbs showed eagerness as the thoughts flashed through his mind, the toad sage nodded. "I want lots of things, but I'll start with the easiest… I want to be released from this cage, I want Kyuubi's chakra unsealed and I want the loyalty and death seal's to be removed from my body" Jiraiya stood for a moment before he spoke "Is that all?" he asked before Naruto smirked, it didn't look right on the face. "For now." Jiraiya stepped forward and spoke "The Kyuubi's chakra can only be unsealed by the Hokage and Tsunade is at the forward command post leading our troops against the invasion" Jiraiya held his hand up chakra gathering "Do I have your word you'll help the village?" The younger ninja watched with interest at the interaction between the Jinchuriki and The Toad Sage. "Would I lie to you god father?" Naruto asked earning silence from the older man.

Suddenly Neji turned and looked back "The Iwa and Kumo forces lead by the Tsuchikage's granddaughter and the Raikage's hand Darui!" he declared causing the younger ninja to take up defensive positions across the large room "You'd best let me out Jiraiya" Naruto said before he moved back fading into the darkness. Jiraiya placed his hand on the bars and spoke "Kai!" he said expelling chakra, as he did the door to the chamber blew open and twenty ninja took positions on the other end of the room, a mix of ninja from Kumo and Iwa all ranging from Anbu to chuunin. Kurosutchi walked past them all and took a position at the front of the pack, she was wearing a red battle dress, her short black hair showed specks of blood, she was followed by a large dark skinned man holding a giant sword "Jiraiya of the Sannin surrender now and find your people spared further bloodshed" Darui spoke, Jiraiya only smiled "Everyone into the cell, the young ninja's eyes widened for a moment before they obeyed, the Iwa Princess snorted "Yes into the barrel little fish" she taunted as Jiraiya backed into the cell and shut the door "You made a mistake coming down here" He told them. The other ninjas were more worried about being locked in the cell with the Jinchuriki than anything else. The enemy ninja relaxed and the Iwa princess walked closer to the bars and looked inside "Was this your plan? Hide in here with the next generation and wait for us all to leave?" she asked and Sasuke smirked "Not exactly" he said looking at her as she turned her angry eyes to him. She opened her mouth the speak and Darui spoke first "Lets just kill them so we can go, we were told not linger" he said and Kurosutchi turned her back to group. It was the last thing she ever did. Suddenly the room was flooded with killing intent and she froze up, she'd felt it of course, she was a seasoned Jonin and the granddaughter of the Tsuchikage.

The Chuunin in the room weren't so lucky, their fear got the best of them, they drove their weapon's straight into their own flesh, some killing themselves while others used it as an opportunity to override the fear with Pain. Suddenly someone dropped down from the ceiling behind Kurosutchi, she turned spinning and aiming a punch at the man, the last thing she saw as those terrifying red eyes as a hand gripped her throat for moment, claws piercing her fair flesh before it was yanked away along with her throat. The Iwa Princess choked to death on her own blood. The alive Iwa shinobi saw the man who had done this. He stood at roughly 6'4, his body was lean and muscular, the body of shinobi. His blonde hair pulled back into a pony tail, his right arm dangling at his side. His legs were covered in black shinobi pants and his feet were wrapped in white bandages. His body was coated in scars, some large and others small, the most noticeable a large scar over his heart. They suddenly rushed forward but the Kumo Shinobi stayed back, Naruto moved with them catching a hurled Kunai and meeting the first shinobi, he ducked a blade from the side and twisted his body, he pushed back on the blade he had blocked and lashed out to the side with kick connecting with the shin of one of the Iwa Anbu, as the man fell forward he turned again dodging a blade from behind and redirecting the blade into the falling man's mask.

The shock of the man's comrade didn't last long as he soon felt the kunai be plunged into his chest and the blade in his hand taken by his killer. Naruto flourished the blade at the three remaining Iwa Shinobi before moved, he appeared in front of them and slashed causing the three of them to fall onto the back foot. He lashed out to the right and spun to the left bring the blade back and driving it into the unguarded stomach of one of his attackers, the man dropped his blade in shock before falling himself, Naruto then moved back twisting his leg to kick the falling blade, the blade was driven into another Shinobi's chest, the last one was shocked as he realised all his comrades had fallen. His shock didn't last long as he felt the same claws that had just killed is commander pierce the skin of his throat with a swift swipe. His blood soon coated his armour and he fell to the ground dead. While the happened the Konoha shinobi were watching on shocked, Naruto had just killed six men without issue, with their own weapons. The man only had one arm!

Sasuke had his sharingan active watching the skilled Shinobi. "So… this is the perfect weapon" He pondered aloud as his fellow shinobi watched him carefully. "This isn't even scratching the surface" Jiraiya spoke as he looked at the young Uchiha". The thoughts of the young ninja were all the same, this thing in front of them was someone their village had sacrificed, for their safety, the Yondaime's own blood reduced to nothing more than a blade for the village to wield. The Kumo-nin watched the last Iwa shinobi fall and Darui spoke "They had you locked away all this time and yet you still fight for them?" His tone was dull despite the small inkling of fear, the man before him hadn't preformed any jutsu and had taken out so many men already. The Iwa princess alone was tough Kunoichi, certainly not someone Darui could've killed so easily. His men gripped their blades as the man in front of him smiled, his blood-stained face seemed to strike fear into them so easily. Suddenly Darui flew into a set of hand seals. "Raiton: Kuropansa" he shouted, the jutsu formed in front Naruto who raised his own hand and flew through three one handed hand seals "Suiton: Suiryūdan no Jutsu" Naruto shouted before spewing out water from his mouth, the water clashed with the black lighting and redirected it upwards causing the roof to collapse down onto them, the room was filled with smoke for a moment before Darui coughed and shouted. "Fall back we must inform the Kage of this!" he shouted before he turned sprinted from the room, his men following close behind.

Suddenly the same empty hall they had ran through seemed to stretch on forever growing longer with every step. A hand gripped his shoulder and Darui turned looking into the eyes of a dead man, his face rotted away and his eyes pale from disuse. Another hand grabbed him, he turned looking at the faces of the men he had killed as they all grabbed him "Come with us Darui!" they chanted as the man began to scream. Darui managed to push through them and turn drawing his blade, he slashed the first man cleaving him in two and then attacked the others. He sliced through them with ease as some ran or others attempted to grab him once more. He reached the last one and he rose his sword striking downwards when suddenly everything flickered, and he realised a terrible truth, one he should've realised in his hysteria.

He'd been in a genjutsu and he'd been killing his own men. Darui collapsed to his knees and screamed in anguish ignoring the approaching footsteps. He'd just slaughtered his comrades. His friends. His men. He felt his head get gripped by his hair and he didn't even bother to fight as his throat was exposed and a blade was dragged over the skin slicing it open. He didn't make a sound as he sat still for a moment blood spraying over the ground in front of him for a minute before he fell into it. Naruto looked down at the man emotionlessly as the blood stained the bandages wrapped around his feet. He looked over his shoulder at the men and women that would've been his classmates had he been normal and smiled, his teeth and face stained red with the blood of the people he had just killed "Shall we?" he asked turning on his heals and began to rush up the steps.

It was silent among the young ninja for a moment before Kiba Inzuka spoke "Fuck me…" he said quietly, his hound barked, Shino spoke up "I believe you speak for us all Kiba, why you may ask? He just killed twelve people without a single thought" the man's talent for stating the obvious almost made the rest face fault. Jiraiya was the first to move after the Jinchuriki and the others followed. As they ran Sasuke could hear the screams of weapon's victims. They arrived at the last door to see him finishing a battle against three Kiri hunter nin's. One launched senbon after senbon at the Jinchuriki without much luck as the other two corralled him with jutsu's into their path. Suddenly Naruto grabbed a kunai from the ground, discarded after one of the earlier battles fought in the room and spun, enhancing the blade with wind chakra and launching it at one of the Kiri Shinobi. His head exploded in red mist as the other two attempted to get over their shock Naruto pounced kicking one in the chest and slashing at the other with his claws. Sasuke moved quickly leaping over Naruto and lashing out with his sword beheading one of the Shinobi as Naruto grabbed a blade from the ground and drove it through the downed shinobis throat pinning him to the ground. Naruto's red eyes turned to the sharingan of the Uchiha and he nearly growled before Jiraiya spoke "Naruto fall in, we are heading to Tsunade" He commanded, the red orbs were turned to him before he nodded and Jiraiya took off, Naruto followed and then the rest of the Leaf Shinobi did too. Soon they were outside, Naruto paused taking in the smell of ash and sounds of chaos a smile turning his lips as the other ninja watched uncomfortably "Oh fresh air and freedom" he whispered loud enough for them to hear. The young ninja exchanged worried glances before they began to run to the Hokage's position.

the village had been divided into sectors and the inner half of the village was still in Konoha's control, their counter measures for invasion allowing them to force attacking nin's though chokepoints they could use to slaughter them. Deep within the village Tsunade Senju stood over a table holding a map of the village a group of Shinobi stood in front of her. Kakashi Hatake, Sharingan no Kakashi. Kurenai Yuuhi, Asuma Sarutobi, Anko Mitarashi, Might Gai were watching her as she looked from the map to the clock and spoke "Dammit he should've been back now..." Tsunade said impatiently, they knew she was talking about Jiraiya. Suddenly a hand clamped over her shoulder and forced her to turn. Her sensei's old face gazed back at her "Have faith in Jiraiya-kun Tsunade" He told her. She nodded closing her eyes. They'd had a moment of quiet and she'd just spent the last three hours healing the wounded, not easy when her apprentice was dragged away by her former teammate to rescue Konoha's darkest secret. Kakashi spoke "Forgive me Tsunade-Sama but where did you send our students?" he asked and Tsunade managed to keep her grimace hidden "They're on a retrieval mission" Was all she said and Kakashi squinted his eye sceptically. Suddenly a chakra spike happened in the centre of the camp and one by one the Konoha 11 dropped one by one, the older generation relaxed until the last person dropped down in front of them. The second Naruto rose his red eyes locked with Hiruzen Sarutobi's own old eyes and the camp grew tense. The adults and Anbu positioned themselves in between the Jinchuriki and the two Hokage. None of them could forget the night the weapon had gone rogue. Especially not Kakashi "You!" The masked shinobi shouted in a fit of rage as his right hand lit up in his signature move and he rushed forward ignoring the shouts of his commander's as he approached the Jinchuriki. Naruto managed one step before his skin was coated in a black ink. The lines seemed to run over every inch of him ending in two seals on his back and chest, easily recognisable as explosive seals. He collapsed gasping in pain as his heart stopped for every second he thought of killing the Copy Ninja. Kakashi was an inch away his hand hovering over the scar on the Jinchuriki's chest when Jiraiya caught his wrist firmly and stopped him from killing him. Kakashi turned his unmasked sharingan to the man and Sasuke could see the fury in his eyes and Sasuke realised how Naruto had gotten that scar. Kakashi had driven the Chidori through his chest. Kakashi struggled for a moment longer before Tsunade's voice boomed through the camp. "Everyone stand down now!" she shouted and quickly moved past the shinobi to look down at the Jinchuriki who held his hand over his heart, even on his knee's and panting the man seemed dangerous, his red eyes finding her own brown orbs. She raised her hand placing it on his head gently and she spoke "Kai!" Her voice was accompanied by a firm pulse and the seals the adjourned his skin seemed to fade away into nothing and the Jinchuriki slumped for a moment. Then a pulse of chakra came from him kicking up the dirt and rubble around him. Another came and everyone moved back as blood red chakra leaked from his skin and onto the ground creating a small whirlwind of red energy. Sasuke could see it, it was hatred, the power of hatred that Itachi had warned him about. Sakura saw power greater than anything she had felt in her life. Hinata saw the power that had saved her life when she was younger. Kakashi saw the power that had taken his Sensei, His sensei's wife and his girlfriend from him. The rest of the assembled saw the power that had nearly destroyed their home. The chakra receded deep into the Jinchuriki and he seemed to tilt forward before he leaned back looking up at the sky and screamed and a red pillar shot high into the sky for the entire village to see.

Outside the village eight people stood silently as they watched the blood red chakra as voices rang deep in their mind all chanting the same words "_The Kyuubi is back, Kurama is back!" _They shouted as the eight Jinchuriki watched the pillar ascend high into the sky before falling back down.

The leaf shinobi watched as the energy was absorbed back into the Jinchuriki and he closed his eyes before he looked up opening his shining red eyes and his lips curled into a feral grin as he spoke aloud "Hello Kurama".

Extra scene I cut:

His last stand.

The root Anbu rolled backwards and dodged a slash from a Kumo Nin and promptly ended his life with a quick move of his blade. He moved again applying chakra to his blade and arms to enhance his strength. He suddenly lashed out with his blade to attack the next man before a fist connected with his masked face. It sent him flying backwards and flipped again landing in a crouch and looking up at the two shinobi in front of him. He couldn't win this fight, he knew that. He stood up from the ground his blank mask falling to the ground and he spat blood from his mouth which was now uncovered. He breathed in shakily and for a short moment he thought he'd heard the voice of his brother. A book fell to ground and it opened showing the unfinished work that he once promised to show his brother. He looked up and grabbed the blade and spoke "You will not pass" he declared and fell into his fighting stance. The group of ninja in front of him looked at him puzzled as he prepared to continue to fight despite his wounds "We have killed your comrades surrender so we can let you live" the ninja said looking at him. The Root Nin paused for a moment and he moved forward.

_"In 'Root"_

_He ducked under a blade._

_"__you have no name."_

_He slashed the man over the stomach but took a blade in the back in return._

_"__You have no feelings."_

_He turned to the man who stabbed him and charged into him tackling him down to the ground and driving his kunai into his throat. _

_"__You have no past."_

_He turned again standing and lunging at the nearest ninja taking a blade to his stomach in order to grasp the man's collar and by extension his neck, then he bit into his neck._

_"__You have no future" _

_He spat the blood and let the man fall, he was stabbed again this time in the leg._

_There is only the mission."_

_He turned and slashed the shinobi who stabbed him over the face before he collapsed down his mask finally falling from his face._

_He didn't remember his name, he'd had several over his life time. He crawled forward and looked down at the book gasping gently as he remembered what he wanted to draw. He grabbed his only brush and dipped it into his pooling blood drawing on the page until he made the image._

_"__Do you see brother Shin?" he asked as he dropped the brush. He let the book fall into his lap and he let out a laboured breath as he closed his eyes "Yes Otouto.. I see" he heard in his head before it all went black._

**_Yo!_**

**_I hope you all enjoyed what is essentially my mind running wild._**

**_The past couple of months I've really dived deep into Naruto Fanfiction and come up with so many ideas._**

**_Forgive the small errors or if its hard to read this is my first go. Fuck knows if ill even update it again. _**

**_I know its not gonna happen but try be nice with your reviews and not just flame me for my take on the Naruto world._**

**_Its an Alternate Universe cause why write about canon when you can just watch it?_**

**_Toodles_**

**_Calzohh_**


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